--- Day changed Wed Sep 03 2008 00:13 -!- elias` [n=me@unaffiliated/elias/x-342423] has quit [Read error: 145 (Connection timed out)] 00:22 -!- elias` [n=me@unaffiliated/elias/x-342423] has joined #hplusroadmap 00:34 < ybit> kanzure, whenever you are through grabbing the vids from superkuh, want to torrent them? 01:29 -!- willPow3r [n=will@cpe-66-75-6-181.san.res.rr.com] has quit ["Leaving"] 02:16 -!- nsh [n=nsh@eduroam-52.uta.fi] has joined #hplusroadmap 02:36 -!- Depucelator [n=Depucela@c-24-118-116-62.hsd1.mn.comcast.net] has quit ["Leaving."] 02:51 -!- Nofaris [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has quit [Read error: 110 (Connection timed out)] 03:31 -!- jm|earth [n=jm@p57B9DD0F.dip.t-dialin.net] has joined #hplusroadmap 04:39 -!- marainein [n=marainei@220.253-204-179.VIC.netspace.net.au] has joined #hplusroadmap 07:13 < kanzure> ybit: Yes. 07:15 < kanzure> http://www.bbc.co.uk/radio4/redesigninghumanbody/pip/lrgnp/ 07:15 < kanzure> http://www.bbc.co.uk/radio4/science/humanalien.shtml 08:38 < procto> I can't wait to start ripping out body parts and replacing them with improved versions 08:38 < procto> I don't use computer from the 80's 08:38 < procto> why does my biology have to be from the 80's? 08:52 -!- Phreedom__ [n=freedom@ip-194-50-167-184.mir.dn.ua] has joined #hplusroadmap 08:53 -!- Phreedom_ [n=freedom@ip-194-50-167-184.mir.dn.ua] has quit [Read error: 110 (Connection timed out)] 09:23 -!- marainein [n=marainei@220.253-204-179.VIC.netspace.net.au] has quit [Read error: 113 (No route to host)] 09:46 -!- ybit [n=h@unaffiliated/ybit] has quit [Connection timed out] 11:08 -!- pk [i=pk@cash-3b-130.res.umass.edu] has joined #hplusroadmap 12:12 < kanzure> ideas on representing reaction kinetics ? 12:12 < kanzure> 'stochastic kinetics modeling of biochemical components' 12:12 < kanzure> is SBML or CellML something I should be looking into? 12:12 < kanzure> http://sbml.org/Basic_Introduction_to_SBML 12:13 < kanzure> http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix 12:13 < kanzure> one of those is a 'stochastic framework' 12:13 < kanzure> BioNetGen http://bionetgen.org/ 12:13 < kanzure> BioPathwise http://bioanalyticsgroup.com/ 12:14 < kanzure> BioNetGen being the free one 12:14 < kanzure> huh: http://www.yeastpheromonemodel.org/wiki/Main_Page 12:14 < kanzure> okay, yeah 12:14 < kanzure> http://bionetgen.org/index.php/Tutorial_Example 12:14 < kanzure> reaction rules are in this document 12:14 < kanzure> but this looks like a small project ... 12:15 < kanzure> those parameters are very useful 12:15 < kanzure> if I could map a database of biobricks to BNGL files. 12:22 < kanzure> http://193.146.190.210:8080/ByoDyn ' Software package for the analysis of paratemer landscapes in biological networks' 12:25 < kanzure> note: /mnt/maxtor/all/Biology/ has http://www.ebi.ac.uk/biomodels/release_21August2008_sbmls.tar.gz now 12:46 -!- Nofaris [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has joined #hplusroadmap 13:12 -!- Phreedom_ [n=freedom@ip-194-50-167-184.mir.dn.ua] has joined #hplusroadmap 13:13 -!- Phreedom__ [n=freedom@ip-194-50-167-184.mir.dn.ua] has quit [Read error: 110 (Connection timed out)] 13:13 < kanzure> http://heybryan.org/projects/cerebellum/ <-- this is a git repo (despite the lack of a .git ending to the name) 13:13 < kanzure> has mostly visual basic .. I apologize 13:13 < kanzure> am forking slowly. 13:14 < kanzure> Haha, 'kinetic simulation and model fitting' is being presented at the old lab as of 15 minutes ago 13:14 < kanzure> which is exactly what Dan and I were talking about 13:14 < kanzure> where is faceface anyway? 13:35 -!- Nofaris_ [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has joined #hplusroadmap 13:50 -!- Nofaris [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has quit [Read error: 110 (Connection timed out)] 14:26 -!- Nofaris_ [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has quit [Read error: 110 (Connection timed out)] 15:58 -!- willPow3r [n=will@cpe-66-75-6-181.san.res.rr.com] has joined #hplusroadmap 16:25 < kanzure> degradation rates, gene expression rates, polymerase per second (PoPS), what else might you want to 'optimize' in a GRN of biobricks? 17:10 -!- ybit [n=h@unaffiliated/ybit] has joined #hplusroadmap 17:25 -!- biopunk [n=p@h91n3c1o261.bredband.skanova.com] has joined #hplusroadmap 17:31 -!- jm|earth [n=jm@p57B9DD0F.dip.t-dialin.net] has quit ["quit"] 17:38 < kanzure> is anybody going to kill me if I just do basic stoichiometry? 17:38 < kanzure> http://bionetgen.org/index.php/Tutorial_Example 17:38 < kanzure> look at "begin reaction rules" 17:38 < kanzure> I'm pretty sure that's just stoich 18:07 * bkero has to do stoiciometry on his car daily. :/ 18:13 < kanzure> buh? 18:14 < kanzure> gas? 18:14 < bkero> Yea 18:14 < bkero> Burning too hot will make gaskets brittle and lose compression 18:15 < kanzure> I should just make it variable for variables to optimize for 18:15 < kanzure> Now I just have to worry about how to make the hidden variable model itself 18:15 < kanzure> Say that I have 10,000 different designs 18:15 < kanzure> and I can simulate all of them and tweak all of them 18:16 < kanzure> now which way do you tweak and such? This is what an ANN would be for, supposedly 18:16 < bkero> ANN? 18:16 < kanzure> but do you just set the exact outputs of the ANN to the parameters for each of the designs ?? 18:16 < kanzure> ANN or hidden markov model or something else 18:16 < kanzure> different ways are possible there 18:18 < bkero> Standardize some of the components of a design and inherit your variable as a class? 18:19 < kanzure> What? 18:22 < bkero> You're trying to find a uniform way to tweak different designs? 18:22 < kanzure> yes, that sounds right. 18:23 < bkero> In an object model, that's what object extension or inheritence is for. 18:24 < kanzure> You mean I've been using object oriented programming incorrectly for the past, uh, decade? 18:24 < bkero> What have you been doing 'wrong'? 18:24 < kanzure> I usually just use hierarchical classes, so I have parents and siblings and so on. 18:25 < kanzure> (class inheritance) 18:25 < kanzure> and then object instantiation is treated just like constructing a new instance of a data struct. 18:28 < bkero> Sure 18:28 < bkero> But you can extend classes 18:28 < kanzure> yeah? 18:28 < kanzure> virtual class members, you mean? 18:29 < bkero> java104/ 18:29 < bkero> http://www.javacoffeebreak.com/java104/java104.html 18:29 < bkero> Virtuals in java are like generics, right? 18:30 < kanzure> Hm. 18:30 < kanzure> I forget. 18:31 < bkero> chizu: Does python have class extension ala java? 18:39 < chizu> Yes, Python is a typical class based OO language. It works more or less how Java does. 18:39 -!- Nofaris_ [n=Nofaris@adsl-75-42-77-105.dsl.scrm01.sbcglobal.net] has joined #hplusroadmap 18:56 < kanzure> ' Fujaba uses Story driven modelling, a graph rewrite language based on PROGRES' 18:57 < kanzure> Still not sure how to do this. Let's say you have 10,000 "CAD" files each doing various permutations and such. Where does the ANN come into play? You could spend a few thousand iterations tweaking parameters on a single file if you had to .. 19:26 < kanzure> 'An alternative idea would be to let the ANN do the prediction of the success of a design running through the simulator. An application of a rewrite rule to the ANN would then cause it to make a possibly better or worse prediction of the results of the simulation. ' 19:26 < kanzure> (well, that's really my text) 19:26 < kanzure> would that be a useful approach? 20:21 < ybit> " [17:16] ANN? " http://en.wikipedia.org/wiki/Artificial_neural_network 20:21 < kanzure> ybit: Did I miss that message of bkero's? 20:22 < kanzure> and what was it in response to ? 20:22 < kanzure> Oh, you're replying to it. 20:22 < ybit> you didn't have a response :P 20:22 < ybit> oh, for your question, not sure if you want my response 20:22 < kanzure> hm? 20:22 < ybit> " [18:26] would that be a useful approach? " 20:23 < kanzure> Heh. 20:23 < kanzure> Do you know? 20:23 < ybit> i do not 20:23 < ybit> unfortunately 20:25 < kanzure> I think I'll just let the ANN predict the results of the simulation of the given model. The input to the ANN has to be "the given model" but you're not just going to dump YAML or CAD into it. You want to dump whatever makes a particular design unique out of the tens of thousands of other generated designs, as the input to the ANN. Now, each time that you generate a new 10k set of designs for some problem, you have to start working with fresh ANNs. 20:27 < ybit> btw, did you ever happen to finish downloading http://www.med.wayne.edu neuropsychopharmacology vids from superkuh? 20:28 < kanzure> No, the download for both fedt and I broke at the same time. 20:29 < kanzure> What makes one design unique? Usually the connectivity between the components, possibly also the parameters for instantiating each part (i.e., if a parameter to a 'nail' is the length of the nail ..). But how do you express connectivity information to inputs of ANN? That doesn't sound right to me. 20:33 < kanzure> Huh, what if it's the permutation ID of the particular design? 20:33 < kanzure> Since it's generating them iteratively .. 20:33 < kanzure> perhaps that's not a good idea. 20:34 < kanzure> Maybe I'll let this be variable -- the input will be the ID of the generated graph; sometimes it will be the seed of the "random number generator" to generate the graph, etc. etc. Then it would be easy to test which ones will tend to have ANNs that accurately predict the simulation results. 20:37 < kanzure> Simultaneously tuning both the type of input to the ANNs as well as the generation of ANNs for problem sets (via picking good 'rule sets' and 'graph grammars' to apply (rewrite rules)) is computationally ridiculous. But only I'd have to tune and test the inputs to the ANNs, and then everyone else would be testing the ANNs for (their new) problem domains. 20:37 < kanzure> unless nsh might have a few ideas 20:37 < kanzure> cough? 20:42 -!- Nade [n=lixasd@cpc2-clif5-0-0-cust516.nott.cable.ntl.com] has quit [] 21:13 < kanzure> When in doubt, make it a variable. Hurrah. 22:08 -!- willPow3r [n=will@cpe-66-75-6-181.san.res.rr.com] has quit ["Leaving"] 22:23 < bkero> $i = 4 22:23 < kanzure> Hm? 22:28 < kanzure> the calculus professor blurted out during his lecture on series (yawn - been here, done that) that he had once attended a lecture of the great Conway, apparently he was demonstrating his tubes.